I have dutifully learnt my kana and some japanese in romaji and I have just bought Clay's 100 Kanji book for my Kindle (love the book, perfect for my next step).Is the いつ the kun-yomi for number 5?What is the .つ which appears after every number written in kun-yomi?These are the kana transcriptions for the kanji on the right-hand side of the page.

Not quite. The kanji can be written without any okurigana, in which case it's read ご. By itself, 五 is "the number 5"; 五つ (いつつ) however is "five (random) items." Most counters will take the onyomi (五本 ごほん "five long thin objects", 五年 ごねん "five years"), a few will take the kunyomi (五日 いつか "5 days") and these you'll just have to memorize.

Just to be clear, and apologies if you already understand this, but it's not normally written いつ.つ; that's just for expository purposes in your Kanji reference book, to separate the reading for the character, with okurigana that is likely to follow that reading (and gives you a clue to use that reading). In real Japanese, it'll simply be written いつつ or 五つ.